Mombasa Marine Park and Reserve is one of the Marine Protected Areas in Kenya established more than ten years ago. The Park is a no-take-zone, while the Reserve is a zone where regulated extractive uses such as artisanal fishing are allowed. Since the year 2004, ecological monitoring of the MPA has been going on aimed at generating information on the MPA status with a view to improve its management. Four year monitoring data (2004 to 2007) of percentage benthic cover using the Line Intercept Transect (LIT) method reveal relatively high average percentage turf could easily out compete and degrade the hard corals and sea grass beds that are important for MPA ecological and biological health status. The growth of algal turf is triggered by nutrient input mainly from land sources. It is therefore important to identify the nutrient input sources into the MPA so as to address management measures to remedy this ecological threat.